Novel techniques for automorphism group computation

Graph automorphism (GA) is a classical problem, in which the objective is to compute the automorphism group of an input graph. In this work we propose four novel techniques to speed up algorithms that solve the GA problem by exploring a search tree. They increase the performance of the algorithm by allowing to reduce the depth of the search tree, and by effectively pruning it. We formally prove that a GA algorithm that uses these techniques correctly computes the automorphism group of the input graph. We also describe how the techniques have been incorporated into the GA algorithm conauto, as conauto-2.03, with at most an additive polynomial increase in its asymptotic time complexity. We have experimentally evaluated the impact of each of the above techniques with several graph families. We have observed that each of the techniques by itself significantly reduces the number of processed nodes of the search tree in some subset of graphs, which justifies the use of each of them. Then, when they are applied together, their effect is combined, leading to reductions in the number of processed nodes in most graphs. This is also reflected in a reduction of the running time, which is substantial in some graph families.

Modelos sin malla en simulación numérica de estructuras aeroespaciales

La presente Tesis Doctoral aborda la introducción de la Partición de Unidad de Bernstein en la forma débil de Galerkin para la resolución de problemas de condiciones de contorno en el ámbito del análisis estructural. La familia de funciones base de Bernstein conforma un sistema generador del espacio de funciones polinómicas que permite construir aproximaciones numéricas para las que no se requiere la existencia de malla: las funciones de forma, de soporte global, dependen únicamente del orden de aproximación elegido y de la parametrización o mapping del dominio, estando las posiciones nodales implícitamente definidas. El desarrollo de la formulación está precedido por una revisión bibliográfica que, con su punto de partida en el Método de Elementos Finitos, recorre las principales técnicas de resolución sin malla de Ecuaciones Diferenciales en Derivadas Parciales, incluyendo los conocidos como Métodos Meshless y los métodos espectrales. En este contexto, en la Tesis se somete la aproximación Bernstein-Galerkin a validación en tests uni y bidimensionales clásicos de la Mecánica Estructural. Se estudian aspectos de la implementación tales como la consistencia, la capacidad de reproducción, la naturaleza no interpolante en la frontera, el planteamiento con refinamiento h-p o el acoplamiento con otras aproximaciones numéricas. Un bloque importante de la investigación se dedica al análisis de estrategias de optimización computacional, especialmente en lo referente a la reducción del tiempo de máquina asociado a la generación y operación con matrices llenas. Finalmente, se realiza aplicación a dos casos de referencia de estructuras aeronáuticas, el análisis de esfuerzos en un angular de material anisotrópico y la evaluación de factores de intensidad de esfuerzos de la Mecánica de Fractura mediante un modelo con Partición de Unidad de Bernstein acoplada a una malla de elementos finitos. ABSTRACT This Doctoral Thesis deals with the introduction of Bernstein Partition of Unity into Galerkin weak form to solve boundary value problems in the field of structural analysis. The family of Bernstein basis functions constitutes a spanning set of the space of polynomial functions that allows the construction of numerical approximations that do not require the presence of a mesh: the shape functions, which are globally-supported, are determined only by the selected approximation order and the parametrization or mapping of the domain, being the nodal positions implicitly defined. The exposition of the formulation is preceded by a revision of bibliography which begins with the review of the Finite Element Method and covers the main techniques to solve Partial Differential Equations without the use of mesh, including the so-called Meshless Methods and the spectral methods. In this context, in the Thesis the Bernstein-Galerkin approximation is subjected to validation in one- and two-dimensional classic benchmarks of Structural Mechanics. Implementation aspects such as consistency, reproduction capability, non-interpolating nature at boundaries, h-p refinement strategy or coupling with other numerical approximations are studied. An important part of the investigation focuses on the analysis and optimization of computational efficiency, mainly regarding the reduction of the CPU cost associated with the generation and handling of full matrices. Finally, application to two reference cases of aeronautic structures is performed: the stress analysis in an anisotropic angle part and the evaluation of stress intensity factors of Fracture Mechanics by means of a coupled Bernstein Partition of Unity - finite element mesh model.

Some consistent finite element formulations of 1-D beam models: a comparative study

A consistent Finite Element formulation was developed for four classical 1-D beam models. This formulation is based upon the solution of the homogeneous differential equation (or equations) associated with each model. Results such as the shape functions, stiffness matrices and consistent force vectors for the constant section beam were found. Some of these results were compared with the corresponding ones obtained by the standard Finite Element Method (i.e. using polynomial expansions for the field variables). Some of the difficulties reported in the literature concerning some of these models may be avoided by this technique and some numerical sensitivity analysis on this subject are presented.

Truncation error estimation in the Discontinuous Galerkin Spectral Element Method

En esta tesis, el método de estimación de error de truncación conocido como restimation ha sido extendido de esquemas de bajo orden a esquemas de alto orden. La mayoría de los trabajos en la bibliografía utilizan soluciones convergidas en mallas de distinto refinamiento para realizar la estimación. En este trabajo se utiliza una solución en una única malla con distintos órdenes polinómicos. Además, no se requiere que esta solución esté completamente convergida, resultando en el método conocido como quasi-a priori T-estimation. La aproximación quasi-a priori estima el error mientras el residuo del método iterativo no es despreciable. En este trabajo se demuestra que algunas de las hipótesis fundamentales sobre el comportamiento del error, establecidas para métodos de bajo orden, dejan de ser válidas en esquemas de alto orden, haciendo necesaria una revisión completa del comportamiento del error antes de redefinir el algoritmo. Para facilitar esta tarea, en una primera etapa se considera el método conocido como Chebyshev Collocation, limitando la aplicación a geometrías simples. La extensión al método Discontinuouos Galerkin Spectral Element Method presenta dificultades adicionales para la definición precisa y la estimación del error, debidos a la formulación débil, la discretización multidominio y la formulación discontinua. En primer lugar, el análisis se enfoca en leyes de conservación escalares para examinar la precisión de la estimación del error de truncación. Después, la validez del análisis se demuestra para las ecuaciones incompresibles y compresibles de Euler y Navier Stokes. El método de aproximación quasi-a priori r-estimation permite desacoplar las contribuciones superficiales y volumétricas del error de truncación, proveyendo información sobre la anisotropía de las soluciones así como su ratio de convergencia con el orden polinómico. Se demuestra que esta aproximación quasi-a priori produce estimaciones del error de truncación con precisión espectral. ABSTRACT In this thesis, the τ-estimation method to estimate the truncation error is extended from low order to spectral methods. While most works in the literature rely on fully time-converged solutions on grids with different spacing to perform the estimation, only one grid with different polynomial orders is used in this work. Furthermore, a non timeconverged solution is used resulting in the quasi-a priori τ-estimation method. The quasi-a priori approach estimates the error when the residual of the time-iterative method is not negligible. It is shown in this work that some of the fundamental assumptions about error tendency, well established for low order methods, are no longer valid in high order schemes, making necessary a complete revision of the error behavior before redefining the algorithm. To facilitate this task, the Chebyshev Collocation Method is considered as a first step, limiting their application to simple geometries. The extension to the Discontinuous Galerkin Spectral Element Method introduces additional features to the accurate definition and estimation of the error due to the weak formulation, multidomain discretization and the discontinuous formulation. First, the analysis focuses on scalar conservation laws to examine the accuracy of the estimation of the truncation error. Then, the validity of the analysis is shown for the incompressible and compressible Euler and Navier Stokes equations. The developed quasi-a priori τ-estimation method permits one to decouple the interfacial and the interior contributions of the truncation error in the Discontinuous Galerkin Spectral Element Method, and provides information about the anisotropy of the solution, as well as its rate of convergence in polynomial order. It is demonstrated here that this quasi-a priori approach yields a spectrally accurate estimate of the truncation error.

Learning Bayesian networks from data by the incremental compilation of new network polynomials

Probabilistic graphical models are a huge research field in artificial intelligence nowadays. The scope of this work is the study of directed graphical models for the representation of discrete distributions. Two of the main research topics related to this area focus on performing inference over graphical models and on learning graphical models from data. Traditionally, the inference process and the learning process have been treated separately, but given that the learned models structure marks the inference complexity, this kind of strategies will sometimes produce very inefficient models. With the purpose of learning thinner models, in this master thesis we propose a new model for the representation of network polynomials, which we call polynomial trees. Polynomial trees are a complementary representation for Bayesian networks that allows an efficient evaluation of the inference complexity and provides a framework for exact inference. We also propose a set of methods for the incremental compilation of polynomial trees and an algorithm for learning polynomial trees from data using a greedy score+search method that includes the inference complexity as a penalization in the scoring function.

Dietary xylanase increases hepatic vitamin E concentration of chickens fed wheat based diet

The study examined the effect of xylanase supplementation on apparent metabolizable energy (AME) and hepatic vitamin E and carotenoids in broiler chickens fed wheat based diets. A total of one hundred forty four male Ross 308 chickens were used in this study. Birds were randomly assigned to 3 dietary treatments (8 cages per treatment of 6 male broilers each) for 14 days from 7 to 21 day old. The control treatment was based on wheat-soyabean meal and was either unsupplemented or supplemented with either 1000 or 2000 xylanase units per kg diet. Orthogonal polynomial contrasts were used to test linear response to dietary xylanase activity. There was a positive linear relationship (P < 0.05) between dietary AME and doses of supplementary xylanase. A linear relationship (P < 0.05) was also observed between dosage of xylanase supplementation and hepatic vitamin E concentration and retention. In conclusion, xylanase supplementation improved dietary AME and increased hepatic vitamin E concentration which may have positive effects on the antioxidative status of the birds.

Modelo de computación conexionista inspirado en las redes de procesadores evolutivos y su aprendizaje

La informática teórica es una disciplina básica ya que la mayoría de los avances en informática se sustentan en un sólido resultado de esa materia. En los últimos a~nos debido tanto al incremento de la potencia de los ordenadores, como a la cercanía del límite físico en la miniaturización de los componentes electrónicos, resurge el interés por modelos formales de computación alternativos a la arquitectura clásica de von Neumann. Muchos de estos modelos se inspiran en la forma en la que la naturaleza resuelve eficientemente problemas muy complejos. La mayoría son computacionalmente completos e intrínsecamente paralelos. Por este motivo se les está llegando a considerar como nuevos paradigmas de computación (computación natural). Se dispone, por tanto, de un abanico de arquitecturas abstractas tan potentes como los computadores convencionales y, a veces, más eficientes: alguna de ellas mejora el rendimiento, al menos temporal, de problemas NPcompletos proporcionando costes no exponenciales. La representación formal de las redes de procesadores evolutivos requiere de construcciones, tanto independientes, como dependientes del contexto, dicho de otro modo, en general una representación formal completa de un NEP implica restricciones, tanto sintácticas, como semánticas, es decir, que muchas representaciones aparentemente (sintácticamente) correctas de casos particulares de estos dispositivos no tendrían sentido porque podrían no cumplir otras restricciones semánticas. La aplicación de evolución gramatical semántica a los NEPs pasa por la elección de un subconjunto de ellos entre los que buscar los que solucionen un problema concreto. En este trabajo se ha realizado un estudio sobre un modelo inspirado en la biología celular denominado redes de procesadores evolutivos [55, 53], esto es, redes cuyos nodos son procesadores muy simples capaces de realizar únicamente un tipo de mutación puntual (inserción, borrado o sustitución de un símbolo). Estos nodos están asociados con un filtro que está definido por alguna condición de contexto aleatorio o de pertenencia. Las redes están formadas a lo sumo de seis nodos y, teniendo los filtros definidos por una pertenencia a lenguajes regulares, son capaces de generar todos los lenguajes enumerables recursivos independientemente del grafo subyacente. Este resultado no es sorprendente ya que semejantes resultados han sido documentados en la literatura. Si se consideran redes con nodos y filtros definidos por contextos aleatorios {que parecen estar más cerca a las implementaciones biológicas{ entonces se pueden generar lenguajes más complejos como los lenguajes no independientes del contexto. Sin embargo, estos mecanismos tan simples son capaces de resolver problemas complejos en tiempo polinomial. Se ha presentado una solución lineal para un problema NP-completo, el problema de los 3-colores. Como primer aporte significativo se ha propuesto una nueva dinámica de las redes de procesadores evolutivos con un comportamiento no determinista y masivamente paralelo [55], y por tanto todo el trabajo de investigación en el área de la redes de procesadores se puede trasladar a las redes masivamente paralelas. Por ejemplo, las redes masivamente paralelas se pueden modificar de acuerdo a determinadas reglas para mover los filtros hacia las conexiones. Cada conexión se ve como un canal bidireccional de manera que los filtros de entrada y salida coinciden. A pesar de esto, estas redes son computacionalmente completas. Se pueden también implementar otro tipo de reglas para extender este modelo computacional. Se reemplazan las mutaciones puntuales asociadas a cada nodo por la operación de splicing. Este nuevo tipo de procesador se denomina procesador splicing. Este modelo computacional de Red de procesadores con splicing ANSP es semejante en cierto modo a los sistemas distribuidos en tubos de ensayo basados en splicing. Además, se ha definido un nuevo modelo [56] {Redes de procesadores evolutivos con filtros en las conexiones{ , en el cual los procesadores tan solo tienen reglas y los filtros se han trasladado a las conexiones. Dicho modelo es equivalente, bajo determinadas circunstancias, a las redes de procesadores evolutivos clásicas. Sin dichas restricciones el modelo propuesto es un superconjunto de los NEPs clásicos. La principal ventaja de mover los filtros a las conexiones radica en la simplicidad de la modelización. Otras aportaciones de este trabajo ha sido el dise~no de un simulador en Java [54, 52] para las redes de procesadores evolutivos propuestas en esta Tesis. Sobre el término "procesador evolutivo" empleado en esta Tesis, el proceso computacional descrito aquí no es exactamente un proceso evolutivo en el sentido Darwiniano. Pero las operaciones de reescritura que se han considerado pueden interpretarse como mutaciones y los procesos de filtrado se podrían ver como procesos de selección. Además, este trabajo no abarca la posible implementación biológica de estas redes, a pesar de ser de gran importancia. A lo largo de esta tesis se ha tomado como definición de la medida de complejidad para los ANSP, una que denotaremos como tama~no (considerando tama~no como el número de nodos del grafo subyacente). Se ha mostrado que cualquier lenguaje enumerable recursivo L puede ser aceptado por un ANSP en el cual el número de procesadores está linealmente acotado por la cardinalidad del alfabeto de la cinta de una máquina de Turing que reconoce dicho lenguaje L. Siguiendo el concepto de ANSP universales introducido por Manea [65], se ha demostrado que un ANSP con una estructura de grafo fija puede aceptar cualquier lenguaje enumerable recursivo. Un ANSP se puede considerar como un ente capaz de resolver problemas, además de tener otra propiedad relevante desde el punto de vista práctico: Se puede definir un ANSP universal como una subred, donde solo una cantidad limitada de parámetros es dependiente del lenguaje. La anterior característica se puede interpretar como un método para resolver cualquier problema NP en tiempo polinomial empleando un ANSP de tama~no constante, concretamente treinta y uno. Esto significa que la solución de cualquier problema NP es uniforme en el sentido de que la red, exceptuando la subred universal, se puede ver como un programa; adaptándolo a la instancia del problema a resolver, se escogerín los filtros y las reglas que no pertenecen a la subred universal. Un problema interesante desde nuestro punto de vista es el que hace referencia a como elegir el tama~no optimo de esta red.---ABSTRACT---This thesis deals with the recent research works in the area of Natural Computing {bio-inspired models{, more precisely Networks of Evolutionary Processors first developed by Victor Mitrana and they are based on P Systems whose father is Georghe Paun. In these models, they are a set of processors connected in an underlying undirected graph, such processors have an object multiset (strings) and a set of rules, named evolution rules, that transform objects inside processors[55, 53],. These objects can be sent/received using graph connections provided they accomplish constraints defined at input and output filters processors have. This symbolic model, non deterministic one (processors are not synchronized) and massive parallel one[55] (all rules can be applied in one computational step) has some important properties regarding solution of NP-problems in lineal time and of course, lineal resources. There are a great number of variants such as hybrid networks, splicing processors, etc. that provide the model a computational power equivalent to Turing machines. The origin of networks of evolutionary processors (NEP for short) is a basic architecture for parallel and distributed symbolic processing, related to the Connection Machine as well as the Logic Flow paradigm, which consists of several processors, each of them being placed in a node of a virtual complete graph, which are able to handle data associated with the respective node. All the nodes send simultaneously their data and the receiving nodes handle also simultaneously all the arriving messages, according to some strategies. In a series of papers one considers that each node may be viewed as a cell having genetic information encoded in DNA sequences which may evolve by local evolutionary events, that is point mutations. Each node is specialized just for one of these evolutionary operations. Furthermore, the data in each node is organized in the form of multisets of words (each word appears in an arbitrarily large number of copies), and all the copies are processed in parallel such that all the possible events that can take place do actually take place. Obviously, the computational process just described is not exactly an evolutionary process in the Darwinian sense. But the rewriting operations we have considered might be interpreted as mutations and the filtering process might be viewed as a selection process. Recombination is missing but it was asserted that evolutionary and functional relationships between genes can be captured by taking only local mutations into consideration. It is clear that filters associated with each node allow a strong control of the computation. Indeed, every node has an input and output filter; two nodes can exchange data if it passes the output filter of the sender and the input filter of the receiver. Moreover, if some data is sent out by some node and not able to enter any node, then it is lost. In this paper we simplify the ANSP model considered in by moving the filters from the nodes to the edges. Each edge is viewed as a two-way channel such that the input and output filters coincide. Clearly, the possibility of controlling the computation in such networks seems to be diminished. For instance, there is no possibility to loose data during the communication steps. In spite of this and of the fact that splicing is not a powerful operation (remember that splicing systems generates only regular languages) we prove here that these devices are computationally complete. As a consequence, we propose characterizations of two complexity classes, namely NP and PSPACE, in terms of accepting networks of restricted splicing processors with filtered connections. We proposed a uniform linear time solution to SAT based on ANSPFCs with linearly bounded resources. This solution should be understood correctly: we do not solve SAT in linear time and space. Since any word and auxiliary word appears in an arbitrarily large number of copies, one can generate in linear time, by parallelism and communication, an exponential number of words each of them having an exponential number of copies. However, this does not seem to be a major drawback since by PCR (Polymerase Chain Reaction) one can generate an exponential number of identical DNA molecules in a linear number of reactions. It is worth mentioning that the ANSPFC constructed above remains unchanged for any instance with the same number of variables. Therefore, the solution is uniform in the sense that the network, excepting the input and output nodes, may be viewed as a program according to the number of variables, we choose the filters, the splicing words and the rules, then we assign all possible values to the variables, and compute the formula.We proved that ANSP are computationally complete. Do the ANSPFC remain still computationally complete? If this is not the case, what other problems can be eficiently solved by these ANSPFCs? Moreover, the complexity class NP is exactly the class of all languages decided by ANSP in polynomial time. Can NP be characterized in a similar way with ANSPFCs?

Ice volume estimates from ground-penetrating radar surveys, Wedel Jarlsberg Land glaciers, Svalbard

We present ground-penetrating radar (GPR)—based volume calculations, with associated error estimates, for eight glaciers on Wedel Jarlsberg Land, southwestern Spitsbergen, Svalbard, and compare them with those obtained from volume-area scaling relationships. The volume estimates are based upon GPR ice-thickness data collected during the period 2004–2013. The total area and volume of the ensemble are 502.91 ± 18.60 km2 and 91.91 ± 3.12 km3, respectively. The individual areas, volumes, and average ice thickness lie within 0.37–140.99 km2, 0.01–31.98 km3, and 28–227 m, respectively, with a maximum recorded ice thickness of 619 ± 13 m on Austre Torellbreen. To estimate the ice volume of unsurveyed tributary glaciers, we combine polynomial cross-sections with a function providing the best fit to the measured ice thickness along the center line of a collection of 22 surveyed tributaries. For the time-to-depth conversion of GPR data, we test the use of a glacierwide constant radio-wave velocity chosen on the basis of local or regional common midpoint measurements, versus the use of distinct velocities for the firn, cold ice, and temperate ice layers, concluding that the corresponding volume calculations agree with each other within their error bounds.